On the positive side, I think the study is much better quality than Haak's, with much more extensive and good quality supplementary materials, many of which are interesting. On the negative side, it totally lacks of any Western European samples, excepted the already known Epipaleolithic ones, being therefore pretty much useless to the understanding of the formation of the modern European genetic pool, except in a negative sense (stuff that is still clearly missing with the Central and Eastern references we have).

This huge blank in Western Europe, who nobody seems willing to fill up, would be quite apparent in the locator map except that it is poorly dissimulated by cutting a good chunk of Europe out of it:

from fig.1

What do we get in this paper then? Lots of info about Central Europe, notably the Carpatho-Danubian region, also about the Greater Caucasus, Siberia and historical Denmark. Add to that a couple of novel sequences from Bronze Age Montenegro and one from Estonia.

Lack-tase

It's interesting in its own way but I'm still demanding Western European ancient DNA. In fact this study (piling up with others) clearly evidences that the Western European, particularly Atlantic aDNA must be key to the understanding of the formation of European peoples. For example:

Something is amiss, right? Well, that is the LCT allele. Bell Beaker Blogger spotted it very well but he could not explain it. So I told him: There are no samples from Western Europe. That's why!

Later I added:

Actually Chalcolithic Basques from the Ebro banks already had more rs4988235-T than any of the samples shown here: 27% overall with as much as 31% in San Juan Ante Porta Latinam.

Notice anyhow that T allele frequency is not equal to "lactase persistance" because, on this allele alone, it may be distributed unequally through individuals (and that's precisely what we see in the Chalcolithic Basque samples, suggesting two different populations). Also there may be other alleles producing the same effect, just that they are not that famous or even known at all.

I must say that the recent finding of similar mtDNA pools to those found in ancient Basques and resembling modern ones in the Seine basin, does reinforce the notion of Western Europe being key, not just for this allele but in general for the conformation of modern genetic pools in much of Europe.

It would seem (Mälstrom 2007) that the Gokhem people (Megalithic SW Swedes) also had some notable LCT frequencies, which are missing everywhere else (in Central-East and Mediterranean Europe, that is) before modernity. Hence the European LCT allele must have expanded from the Atlantic.

Y-DNA

It's not the only this particular trait, mind you. For example, another detail that Bell Beaker Blogger spotted in this paper's data, is that the first known modern S116-derived is in a Bell Beaker individual. Not in Yamnaya, not in Corded Ware, not in Unetice... but in the Bell Beaker carriers that (culturally at least) came from the Southwest.

Specifically it is R1b-U152 (alias S28), which has sometimes been dubbed the "Celtic" subclade because of its distribution across the Alps, being particularly important in Switzerland and North Italy (including non-Celtic regions like Tuscany, Piamonte and Liguria, as well as Corsica). It has also some notable presence in much of France, SW Germany and Belgium.

I already argued back in 2010 that R1b-S116 must have expanded from Southwestern Europe, possibly Southern France. No need to extend myself on this matter because there has been nothing new in all these five years (sadly enough). Just attach some old maps here for your convenience:

Frequencies of the main European R1b subclades: S116 (red) and U106 (blue)

ADMIXTURE

Hidden deep in the supplemental materials there is sup. fig. 6, which is an ADMIXTURE analysis of ancient and modern sequences. I simplified it by removing modern Asian and African samples as well as low K scores, all them pretty much irrelevant, adding more clear labels and rotating it:

The most interesting aspect is that this analysis pretty much gets rid of the exaggerated Yamna influence attributed by Haak, bringing it down to much more acceptable levels. Even Corded Ware peoples were, it seems now, only weakly related to Yamnaya and much more strongly related to Paleo-European hunter-gatherers (tan) and Mediterranean early farmers (yellow). Some of the Caucasus (teal) component was anyhow already present in pre-Indoeuropean farmers from Hungary and it is only the minor Siberian element (blue shades) what really marks the distinctiveness of Indoeuropeans.

Notice that in this analysis, early European farmers like Stuttgart are not single color but dual: they appear as almost exactly a 50-50 mixture of Paleo-Europeans (tan) and Mediterranean farmers (yellow). The only (almost) true yellow reference are Naqab Bedouins, pointing again to a PPNA origin of the migrant farmers, who, after admixture with European aborigines, surely in Thessaly, spread the Neolithic through the subcontinent.

When, at K=19, the Naqab Bedouins form their own distinctive component (pale yellow) the yellow component suddenly expands in all other samples at the expense of the rest. It changes meaning at that point, beware: it has become the Sardinian component, although one can well argue that this component is very much dominant among early European farmers (but always mixed with some Paleo-European, some Caucasus, some Bedouin even), there is not any single sample that is clearly dominated by it at >80% frequencies (visual estimate), only Sardinians score that high. Admittedly it'd be interesting to re-run this without Sardinians and see what happens.

From the Basque origins viewpoint, I find notable that (again) the Basque and Swedish farmer sequences are similar all along. The latter have more yellow component however, implying that Basques are even more Paleo-European than they were.

In contrast, in extended data fig. 6, Basques appear as less related to WHG than our immediate neighbors (Spanish and French), what is probably an artifact of Indo-European admixture in the latter, as Indoeuropeans were no doubt largely Paleo-European and the Siberian elements they carried may also weight in that same direction. This is also visible in the ADMIXTURE graph above: French clearly carry some more tan Paleo-European, in addition to the Caucasian teal (and in some K-values also minor Siberian blue shades).

In general we see an apparent increase of the Paleo-European component as we move away from the Neolithic but while in the French case this can be partly attributed to Indoeuropean flows from, ultimately, Eastern Europe, in the Basque case that is not the case. There must be another source of that excess Paleo-European element and that source must necessarily in Atlantic Europe.

1. The trait is shared by Yamnaya and Corded Ware. It is present in modern IEs like French but absent in modern Basques.

2. The trait was not present in "peninsular" Europe (i.e. West of the Gdansk-Odessa isthmus) before the Kurgan expansion era. The only exception is La Braña but this WHG has always got minor affinity issues, probably because of low coverage, so I would not read too much on it.

Said that, the trait was probably present in Eastern European HGs, who make up the genetic backbone of PIE. This is apparent in the Pitted Ware individual and to lesser extent the Motala SHG, as such it should be considered loosely akin to the much debated "ANE" component (although it is obviously much smaller). It's probably also interesting, for people with a more eastern focus than mine, to explore the meaning or affinity of the various shades of "Siberian blue", I just did not have the time nor thought it was too important.

On the contrary the Highland West Asian "teal" component was present in Hungary Neolithic at least (less strikingly obvious in other early farmers), so it can't be considered to be strictly IE and rather suggests some "Anatolian" element already in the Thessalian Neolithic, but minor anyhow.

Also in populations like Greeks the teal component can surely be attributed to a great extent not to the Indoeuropean immigration but rather to the "Pelasgian" immigration from Anatolia of Vinca-Dimini peoples (Halaf related, affecting only parts of the Balcans, with mixed offshoots as far as East Hungary and Slavonia, probably affecting Italy too later on, but not beyond). The lack of "Siberian blue" seems to favor this interpretation.

What is You opinion on the R1a of Sintashta? one is Z-2124 and the Other is Z-645 so far according to Genetikers analysis.https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/Do you think it has European Origins? and what about the massive WHG ancestry of them?.

:) One is listed as R1a1a1b-S224/Z645 and the other R1a1a1b2a2-Z2124, So one is Ancestral to Both European Z-283 and Asian Z-93 the other is specifically Asian or SC Asian Z-94 derived!other matter is the Autosomal structure which show massive EHG like structure, so we should say?

Marnie:I'm thinking the the teal component looks PIEish, but that the more intense blue and light blue look Uralic associated.

@Maju:On the contrary the Highland West Asian "teal" component was present in Hungary Neolithic at least (less strikingly obvious in other early farmers), so it can't be considered to be strictly IE and rather suggests some "Anatolian" element already in the Thessalian Neolithic, but minor anyhow.

Marnie:I don't know about this. Teal component also looks to be present in Montenegro Bronze age.

The Siberian blue may indeed be also and even more strongly associated to Uralic but when we compare Estonians and French we see only a very mild difference in this aspect anyhow and we also see the blue shades among Adygei, for instance, so it's something more generic. Obviously PIE and proto-Uralic (or proto-FU) were in tight contact and they may have overlapped once and again, also Siberian haploid markers (mtDNA C) are seen in Neolithic Ukraine, which is not generally imagined as a proto-Uralic area: I'd say that some of the "Uralic" element (more apparent because of its distinctiveness) was carried around by IE speakers within the Kurgan expansion process.

"Teal component also looks to be present in Montenegro Bronze age".

But Bronze Age is already posterior in time to the first Kurgan expansions, so it can be seen as less surprising. I haven't checked exact timeline, culture or whatever other factors, why would you think that it is also significant? It was in the Bronze Age (since c. 2000 BCE) when the IE Greeks invaded Greece, so offshoots could well have gone to Montenegro for all I know, really.

@Nirjhar: "One is listed as R1a1a1b-S224/Z645 and the other R1a1a1b2a2-Z2124, So one is Ancestral to Both European Z-283 and Asian Z-93 the other is specifically Asian or SC Asian Z-94 derived!"

Looks Asian then. But don't want to dig too much on the matter. Notice that today even the Samara area has R1a of Asian centrality (and clearly derived from Central Asian precursors, not the other way around), regardless that it is technically in Europe (would be its border for ancient Greeks). So the Sintashta area, which is farther to the East should be Asian too.

"other matter is the Autosomal structure which show massive EHG like structure, so we should say?"

Could be something like EHG-dominated, I guess. It's hard to associate Y-DNA with autosomal DNA in many cases. A good example are North Africans, dominated by clearly African Y-DNA lineages (E1b variants) but autosomally (and largely also mtDNA-wise) mostly West Eurasian. Another such example could be Native Americans before Ma1 was known, whose autosomal DNA and mtDNA pool look totally East Asian but their Y-DNA is clearly derived from Iran or somewhere nearby. Or Western Uralics, who are almost 100% European in the autosomal and mtDNA aspects but have huge amounts of Y-DNA that comes from the Far East. I would guess that R1a and related autosomal genetics behave similarly, implying a patrilocal expansion with massive and repeated absorption of women from other backgrounds.

Again, I agree. I'm absolutely interested in these results. I'm just trying to understand why they happen while at the same time they break other models completely.

"Also, I think it's time to scrap the ANE-WHG-ENF model."

Yes, probably. But cross check the qpAdm results with the ANE-WHG-ENF model. What happens? A population with high levels of WHG goes to South Asia and from the mix: There is a sharp increase in ANE and a very sharp decrease in WHG (that almost disappears). So I'll say it again: what if ANE is just a composite of WHG+South Asian? Wouldn't that explain why we're not finding WHG in places that according to the steppe hypothesis (and to these qpAdm results) should have a good amount of it?

Now let's see about the Near East. EEF had WHG levels starting at 25-30% and no ANE. Ancient Anatolians (and probably Transcaucasia, Syria, North Levant, North Mesopotamia) could not be far from those levels. And then when ANE appears, WHG disappears.

Why Moroccans (who lack ANE) do instead keep some good 15-20% WHG?

And why do Basques, who are south Europeans, have North European levels of WHG, when coincidentally they have very low ANE? Similarly Spaniards have more WHG and less ANE than other south Europeans.

Haplogroup R has a clear South Asian origin. And when R appears in North Eurasia (WHG territory), ANE appears at high levels and WHG decreases sharply.

Why EHG would never show as admixed between WHG + MA1 (who believed to be pure ANE)?

So I think this hypothesis is worth a look, because if we discover that ANE is WHG+SE, it could be a breakthrough to understand prehistory.//So what do you think? is it tenable?.https://www.blogger.com/comment.g?postID=6523661672842294682&blogID=4123559132014627431&isPopup=true&page=4

"Specifically it is R1b-U152 (alias S28), which has sometimes been dubbed the "Celtic" subclade because of its distribution across the Alps, being particularly important in Switzerland and North Italy (including non-Celtic regions like Tuscany, Piamonte and Liguria, as well as Corsica). It has also some notable presence in much of France, SW Germany and Belgium. I already argued back in 2010 that R1b-S116 must have expanded from Southwestern Europe, possibly Southern France."

It is good to read some well-researched information other than the seemingly-endless "mass migration from the steppe" perspectives on the other genetics blogs.

Incidentally, R1b-U152 is also found at notable frequencies in Morocco, Algeria, Tunisia, Sardinia, and Sicily.

Can you document its presence in NW Africa? I know that there is some R1b and that part of it is of European origin but never imagined it'd be this particularly clade, otherwise spread north and east of the Pyrenees.

But precisely that it is U152 and not other more "Iberian" lineage makes it inconsistent with Megalithism, unless it arrived directly from France, and even then. The overall frequency is tiny but relative to R1b it is massive, comparable to what we see in Switzerland or North Italy. The only Megalithic explanation to my eyes would imply a jump from Corsica (or maybe some other not yet properly studied region?). In any case it looks like a strange micro-founder-effect.

"R1b-S116 must have expanded from Southwestern Europe, possibly Southern France"

Not that I have astrong conviction on this matter, it any claim I have studied it hard, but S116 looks like it expanded from the Rhine-Danube interglacial/ west Alpine region (~ Swabia). Look at its phylogeny . There is nothing geo- central about southern France .

What about L238, DF99, and DF19? I'm pretty sure all of those are specific to Central Europe. Central Europe also has the rest of the P312 subclades and a basal L11 clade(Independent of U106 and P312). Unless L11 and P312 are not defined well(Lots of undefined L11*, P312*), the greatest diversity is in Central Europe for both.

Do you really think that any of these r1b lineages underwent single step unidirectional expansion processes? That's what you get spending all your time kibitzing with Wolfgang. Makes you dumb after a while.

@Krefter: irregularity in the study of lineages by private commercial agencies in different parts of Europe (or anywhere else) is meaningless. Those lineages are as relevant as any other under the "asterisk". And there is a lot of unresearched S116* SW Europe.

Also I'm not talking L11 bu S116/P312: L11 and precursors may well have more eastward origins but the paragroup (xS116,U106) is very minor in size again, so it's just like a thin umbilical cord linking these two major subhaplogroups to the more remote West Asian origin of R1b in general, and we can't say much about it: just a trickle of connexion between West Asian primary R1b expansion and West European secondary S116/U106 expansions.

@Maju,"Those lineages are as relevant as any other under the "asterisk". And there is a lot of unresearched S116* SW Europe."

If that's the case, then that supports a SW European origin for P312. I'll email the authors of an upcoming paper with Neolithic Spanish genomes and ask about Y DNA. 3000BC SW France, no P312. I think Ancient DNA has already spoken for itself on this matter.

Not really: there is only one pre-BA individual with this lineage and is Bell Beaker culture, which stems from SW Europe. In comparison with Central and Eastern Europe there has been almost no Y-DNA research in SW Europe, just a few samples from the Mediterranean basin.

I hope you're right because I've been waiting without almost any news in the relevant aspects of this research for at least half a decade. Nothing relevant has been published on European R1b since Myres 2010 and Morelli 2010, and those papers were already demanding a follow up, mind you. Too much of today's haploid research has fallen in the inadequate hands of private corporations, whose customers are massively from affluent and "racially conscious" Germanic Europe. So they detect and even dare to name minor lineages in Sweden but the bulk of the haplogroup, which is certainly not in Sweden, remains unresearched altogether.

Anyways, I do not understand the logic behind the "steppe hypothesis". I can understand (up to a point) the Neolithic hypothesis via the Balcans, Danube and Mediterranean but no idea how can the steppe be inserted into that, really: it's like inserting a chunk of the Sahara in the middle of the Amazon.

The Neolithic hypothesis for me is lacking because it can only work IF and only IF there were secondary MAJOR expansion centers in Western Europe (one in the SW and the other, less important, in the NW). So, in order to work, it needs to be integrated with a theory of the Atlantic Neolithic and Chalcolithic and nobody is doing that (except myself).

To be honest, Maju you appear to have a bias against the idea of massive gene flow from the East.

I don't understand how you can be so critical of massive gene flow from the East when we have prove in Ancient DNA, but feel so strongly about gene flow from the Atlantic when there isn't much evidence. Atlantic and Central Europe in 3,500BC were basically the same people, so it'll be hard to find evidence of gene flow from one to the other anyways.

A few months ago you insisted Andronovo were not Yamnaya-like and their R1a was of local Asian origin. Well, now we know Andronovo/Sintashta were just like Corded Ware(Descendants of R1a-S224 carrying Corded Ware-like people) and carried Z93. It's just a matter of time such convincing evidence is found for an Eastern origin of R1b-L11 and P312.

I do have a "bias" (actually a much meditated judgment, rather than a prejudice) against "massive gene flow" from anywhere: it's not so easy to replace established farmers as North Americans seem to think just because they displaced the Native Americans with industrial means. Notice that almost all the European migration to the Americas is post-industrial: earlier there was just not enough people willing to emigrate at all, let alone means to displace or massacre so many people in planned form. It was also based on a very developed agricultural base, allowing for unprecedented masses of dispossessed farmers to be relocated to colonial grounds.

But what you're telling me is the opposite: that a bunch of nomads from the semi-desert or steppe replaced masses of farmers overnight. That's a very exceptional claim and therefore demands exceptional evidence, not just your camarilla wishful group-thinking.

Additionally, your claim (which is not even clearly stated, making it more difficult to discuss) is mostly based on cherry-picked studies of autosomal DNA, which tell nothing about Y-DNA on their own. Autosomal DNA for its very nature, must be processed with approximative statistical analysis tools, which are subject to be affected by the preliminary decisions such as the sampling strategy, the tests to be performed, etc. Therefore not just one but several different studies must be considered, as they allow us to see the problematic with sufficient perspective and not just from the particular angle of one specific paper. Most studies do not support "massive" replacement, just some. And that's a big difference.

"A few months ago you insisted Andronovo were not Yamnaya-like and their R1a was of local Asian origin".

Did I? I don't recall. Anyhow, Nirjhar just underlined that effectively the Sintashta sequences are not probably derived from European clades. So... it would seem that my processing mind is better than my memory: I was right (it seems) even if I don't recall saying that.

"It's just a matter of time such convincing evidence is found for an Eastern origin of R1b-L11 and P312".

LOL you call that "convincing"? Anyhow, for as long as researchers keep studying the East and ignoring the West they will not find the origins of Western R1b. Some day even the most fanatic ones will realize.

"To be honest, Maju you appear to have a bias against the idea of massive gene flow from the East."

Get real. Researcher Paul Heggerty is essential flaggin many problems with the Steppe hypothesis.

It not surprising that Luis is specifically interested in Iberia. He lives in Bilbao, after all, an acknowledged center of Basque culture.

I also noticed you accusing Gioiello of being an Italian nationalist because of his Italian Refugium theory.

It's a little bizarre for you, Krefter, to be going be going around accusing Gioiello of being some sort of Italian nationist conspiricist, and Luis (Maju) of having "a bias against the idea of massive gene flow from the East."

Even the Allentoft paper doesn't agree with massive migration from the Russian Steppe as the sole source of PIE.

So, Krefter, I suggest you tone it down, or you and your conspirators may find yourself under investigation.

Krefter, To prove that Those Z-93+,Z-94+ lineages of Sintashta,Karasuk,Andornovo etc are from Europe we need1. Absence of R1a-M417 lineages Copper-Bronze age Samples of SC Asia etc.2. Emergence of those lineages in at least one archaeological cultures in Europe around 2000 BC or before.Although the first observation is the key to all.

@Marnie: the case of Gioello is interesting because he's clearly too obsessed with Italy and he does tend to cling to burning nails, however he's clearly interested and, even if he may be wrong, he does point to issues that others may just ignore. He's too Italocentric for his own good BUT he studies the matters in great detail and now and then provides evidence of interest - not enough to support his case, but that in some cases may well be a good counterpoint to Nordicism or other biases that plague this field, especially among amateurs.

The problem is that Gioello is one person (rather reasonable in my experience in spite of his obsession), while the Nordicists and other Indoeuropean Nationalists are legion. And just by numbers they seem to feel stronger and grow arrogant in some cases. They gather in their forums and agree to their own wishful thinking and then go around feeling that it is unfair that some other people object to their camarilla consensus.

But it is not only fair, it is necessary.

As for I having a focus in SW Europe, it is, as you correctly say, only natural, much as Finns seem to have an interest for their region and Uralic macro-ethnicity (and normally I get along with them: our focuses are complementary). It is also good because it offers a counterpoint to the Indoeuropean Nationalist horde.

But what matters are not accusations of bias, unless they are well supported (otherwise they are just mild personal attacks), what matters are facts. And I would like to discuss facts here above everything else. I'd appreciate much better the Nordicist horde if they'd bothered arguing their hypotheses properly and paying due attention to counter-arguments. That would be a productive discussion indeed, in which we would all learn. There's something of it but it's negatively affected by the obsession some have to get their prejudice "proven", their bet "won" by cherry-picked studies or data bits. Instead of trying to find the Truth, or at least approximate it as much as possible, they try to impose their own "truth" (dogma, prejudice, wishful-thought) stepping out of proper scientific debate, which requires open minds, and stepping a bit too close to pseudoscience.

I'd beg the theorists of the massive late replacement from the steppe to have a more scientific and less warrior-dogmatic attitude.

@Nirjhar: I disagree: there's no way to prove that Z93 is from Europe, unless maybe they'd found it in significant amounts and ancestral haplotypes in Europe itself, what surely won't happen ever. Z93 is clearly an Asian lineage that spread from Iran or somewhere nearby (AfPak maybe) in Northern direction. Z93 is evidence of the "Asianness" of Sintashta in the Y-DNA aspect. They were probably just acculturized by neighboring IEs from the West.

Yes and Sintashta also seems to have BMAC influence from the South so it will be Important to see if BMAC shows R1a-Z93 etc or not.OTOH there is a recent funny paper arguing for the Steppe Origins for R1a1a and R1b1a2 -http://biorxiv.org/content/biorxiv/early/2015/06/15/020933.full.pdf

Marnie,//I also noticed you accusing Gioiello of being an Italian nationalist because of his Italian Refugium theory.//You are not seriously accusing me to be Krefter are you? it is absolutely ridiculous.

Thanks for the comments. The point is not whether I agree with Gioiello or not, or you, but the issue of bullying, targeting and attempting to discredit members of the public under pseudonyms.

This pseudonym users are not mere amateurs. Most of them on eurogenes and the anthrogenica forum are paid professionals working anthropology and genetic anthropology at top institutions. You can tell by the fact that they have access to data sets before they are published and by the content that they blog about that then gets into publication and that is then instantaneously highly publicized popular press.

"You are not seriously accusing me to be Krefter are you? it is absolutely ridiculous."

Some of papers that you and your cronies at the Genographic Project and Harvard Medical school have colluded on have been funded in part by NIH and US federal research dollars. We can tell that by the recent Haak paper. Therefore, a federal investigation could be launched to find out exactly who you are: Nirjhar007, Krefter, Balaji, Chad Rohlfsen, Mike Thomas, Davidski, Ryu, Colin, Alberto, Seinandzeit, Simon_W, eurologist, capra internetensis, etc.

So, whether you think what I am saying is ridiculous or not, is irrelevant.

Your right though: blogging under pseudonyms for more than five years trying to construct a phony baloney Mass Migration from the Russian Steppe theory for the only origin of PIE languages and people is quite ridiculous.

Marnie: if you want to throw unfounded accusations around, do it elsewhere (and document them scientifically if you want to be believed).

Nirjhar: if you are bringing issues from other forums here, do not.

Last word on the matter: the comments from you two will be throughtly read and NOT PUBLISHED if you continue with this. The only continuity statements on this I will admit are of the kind "I'm sorry, I've been a jerk".

Thank you in advance for your future behaving like good scientists, who keep it polite, do not invade other people's space (this is MY fucking blog, go scatter your crap elsewhere), and document their claims with good evidence.

Important note to Marnie: I can't believe a word of your paranoid accusations because: (1) they don't make sense (these guys are mostly amateurs for sure and they are different people in most cases: you can see how they behave distinctly year after year - it's not so easy to perform in text - unless I guess if you have a very well organized multiple personality disorder), (2) I have yet to see a single piece of evidence (and I have asked you to show them several times). The easiest one to fool is yourself, Marnie. Prove your fucking claims or shut up!

National Science Foundation (HOMINID grant BCS-1032255), U.S. National Institutes of Health (GM100233), Howard Hughes Medical Institute, Australian Research Council (DP130102158) and German Research Foundation (Al 287/7-1 and 7-3, Al 287/10-1 and 14-1, Me 3245/1-1 and 1-3).

My guess would be that all the three main groups in Europe (yellow, tan, blue shades) are just different Homo Sapiens/Homo Neanderthalensis admixtures (or different Neanderthal races), and that they actually tell us very little about how "European" (Neanderthal) these peoples are.

If you want to find out how European people in Europe are today, you should look for Neanderthal features instead: blond hair, blue/gray eyes and very light skin. Possibly also red hair, because that seems to be a very old mutation resulting form the mixing of Homo sapiens and Neanderthals.

No, that's not how things work. There's been many studies on many of these ancient samples already and the Neanderthal admixture apportion is like modern one. The only exception is Ust Ishim, which is very ancient and seems to have its own extra local Neanderthal admixture event, but which left no significant legacy anyhow.

This is not the proper thread to discuss Neanderthal admixture but just for the record:

(1) I don't think that pheomelanin prevalence variance (which is what causes red hair in low eumelanin but is also present in people with high eumelanin, i.e. tan to black, causing only a more reddish or less yellowish color in the skin normally) is related to Neanderthals at all. Some Neanderthals did also have pheomelanin producing alleles but those were different from the ones found in our species.

(2) On the contrary I do suspect that straight hair is a Neanderthal inheritance. At the very least Neanderthal keratin alleles have been selected for among Eurasian H. sapiens, so skin, nails and hair should tend to be similar to those of Neanderthals (not in color but in texture) and the most obvious texture innovation in this aspect is straight hair (the original H. sapiens hair texture was almost certainly curly, probably Afro-curly).

I don't know if this is of interest to you Maju, but as you are discussing similarity of Corded Ware to Early European Farmers, slightly concerning for Haak's conclusions, I was having a look through their supplement and noticed this figure, S7.11 -

http://i.imgur.com/7zJPVPM.png

It explains as follows:

S7.11a - f4(European, CW;Yamnaya, Chimp) is negative for all Europeans. This means all Europeans are further from Yamnaya than CW is.

S7.11b - f4(European, CW;Karelia_HG, Chimp) is negative for all Europeans. This means all Europeans are further from EHG than CW is.

Both of these are as expected, based on Haak's conclusions.

S7.11c - f4(European, CW;Loschbour, Chimp) is negative for all Europeans, except Northern Europeans and Basques for which it is positive. This means all these N Europeans and Basques are closer to WHG, or no different than CW is.

Now, the confusing one (at least to me):

S7.11d - f4(European, CW;LBK_EN, Chimp) is actually negative for all Europeans, except Sardinians, Basques, Bergamo and French_South. This means that only these Europeans I've mentioned are actually closer to LBK_EN, the Early Neolithic, than CW is. Populations like Spanish, Croatian, Sicilian, Icelandic, English, are actually further away from the EN compared to CW.

It's tough to see how this fits with the idea that the predominant dynamic in Europe is a tradeoff of LBK_EN to Yamnaya ancestry, with the theory being that CW have less LBK_EN ancestry than many modern European populations, when these modern Europeans are actually further from LBK_EN.

When it comes to this paper, the CW is found to be between Yamnaya and LBK_EN on many measures relating to third populations, such as Native Americans... Thus their inference that it was Yamnaya admixed, and the various creative f4 statistic based measures they use to gather this information to quantify this effect to find ancestral contributions.

But at the same time, this stat in S7.11d appears to be placing Corded Ware as either exactly as close to or closer to LBK_EN as most present day Europeans....

Your statistics basically seem to imply (with the usual caution) that there are late exogenous inflows after the Corded Ware period (or even in parallel maybe). Most of those inflows would be Mediterranean, IMO, and might be related to the relative abundance of Y-DNA J2, so far undetected in the early farmers of Thessalian roots.

Would this explain your problem? I think it does. Those extra Mediterranean influxes would begin with the Vinca-Dimini invasion, affecting originally only the Balcans, although irregularly so. From either these "Pelasgian" Balcans or from further East (Anatolia, Cyprus maybe) there were a number of waves some attested, others suspected. Later came the Mycenaeans and the other Sea Peoples, including the Tyrsenian migration westwards, then the Phoenicians, followed by the Greeks and finally the Roman period, which must have redistributed populations around, especially settling veteran legionaries and also whoever survived the often very harsh slave trade conditions.

But overall this must be, excepting Balcans and maybe parts of Italy, a rather thin layer or layers. So my question is: they are more this than that... but how much more? Probably not much.

Maju,Have you seen this: http://yhrd.org/tools/branch/R1a-Z2124from the ancestral branches, it seems R1a comes from West Asia, between Iran and Turkeythe map above shows that SNP is spread also in Indonesia! Western Asia can be the area where R1a and R1b split and Central Asia where R1a started to bud, I think Uralic people had an important migration from Iran, Caspian area, as suggested from archaeology Already in the Mesolithic of the Urals has similarities with Zarzian and Caspian, and the first herders came from the south BTW i'm very sure that R1 and R2 Split happened in SC Asia or Near by.

That R1a first spread from Highland West Asia was already settled by Underhill 2014, and I have been backing that paradigm all the time. That's also true of its Z93 subclade. I'm not sure why Z2124 seems so important to you, being part of Z93.

"I think Uralic people had an important migration from Iran, Caspian area, as suggested from archaeology Already in the Mesolithic of the Urals"...

I think you are confusing (proto-)Uralics with something else (maybe proto-PIE). Judging on the overwhelming Y-DNA evidence and also some archaeological data, ancient mtDNA, proto-Uralics were a Taiga specialist people who migrated westward from the area of Mongolia or North China since the Last Glacial Maximum, arriving to Europe most likely in the Epipaleolithic, and maybe even bringing the pottery technology (very old in East Asia) with them to West Eurasia.

If there were population expansions along the Atlantic coast sparked by founder effects from people with mixed steppe, farmer and HG ancestry then the resurgence of farmer and HG dna might have come from that.

Yes, there is a lot of material in this paper. This makes it a bit more difficult to digest but also much better quality than for example Haak's, which I found lacking in the supplemental material (the standards set by Lazaridis et al. and other papers like the Neanderthal admixture ones are very high but probably necessary in order to demonstrate that the work is well done, using all possible approaches, testing possible misunderstandings, and documenting almost every single step).

This could be of interest to you guys and could shed some new light on the beginning of agriculture in Europe. Blagotin culture, the place where Mediterranean grain agriculture was adopted to Continental European climate. This culture is predecessor of Vinca culture and indicates that from the 6th millennium BC, grain agriculture and metalwork could have moved north west together from the Balkans...

Very interesting article, even if maybe a bit speculative at some points, thank you for sharing. Starcevo culture is not however direct precursor of Vinca unless you disdain the fact that the Vinca-Dimini implied a major cultural change in the whole area, that destruction of settlements seems to imply invasion and that the actual precursors of Vinca-Dimini seem to be in Anatolia/Kurdistan (Can Hassan and Tell Halaf).

The organization of the earliest layers of vinca settlements is the same as the one in Blagotin and other Starchevo sites. This suggest that Starcevo and Vinca were the same culture at the beginning of Vinca. I don't think we can talk about the invasions here which caused the replacement. Just continuation with evolution caused by merging. It is the same as asking if Anglosaxons and today's British people are the same culture. They are and they aren't...

The article has to be speculative :) We actually have no idea what was happening in the Balkans at that time. But i did keep the speculation as close to the archaeology as possible.

Anyway just thought you might like to know this as there is virtually no info on this archaeological site.

Well, your conclusion is not generally accepted. Most prehistorians think that Vinca-Dimini is intrusive: burning of some settlements, foundation of new settlements, reorganization of old settlements in what some have argued is a hierarchical structure, fully new pottery style (total change in colors, from red-white or red-yellow to black-beige), new ritual iconography, such as the famous Vinca "venuses" but also the first appearance of male idols, etc. However it's probable that part of the Painted Pottery population and their cultural substrate survived under the new masters and that talking about mass population replacement is an exaggeration. It's surely just a new layer, a substantial one though, one that displaced the Balcans from tending to Palestine/Arabia (as early European farmers did) to tending to Anatolia/Caucasus.

"It is the same as asking if Anglosaxons and today's British people are the same culture. They are and they aren't..."

It's rather like asking if the builders of Stonhenge and modern Britons (or Celtic Britons also) are the same culture: they are not, even if there is almost certainly a great degree of genetic continuity and some cultural elements did somehow get through. There were Indoeuropean invasions in between (Celts, Romans and Germanics) that changed almost everything in terms cultural and linguistic.

"But i did keep the speculation as close to the archaeology as possible".

Fair enough. I really like the article, even if I disagree with you in some key points.

The information about the identical organisation of settlements in Blagotin an Vinca sites is virtually unknown in the international archaeological community. So I am not surprised that the replacement theory is the generally accepted one. What I find amazing is that we have no ancient genetic data for the early Balkans cultures....

do you plan to do a follow-up on this post and the Indo-European question in general? I'd be very interested to know your thoughts on the high relatedness of modern West Eurasians and Yamnaya many have observed. Do you think that perhaps European HG ancestry and/or purported iron age migrations of 'teal' lead to an inflated steppe affinity? Would it be possible that there was a major recurrence of the Paleo-European component (whether it be as HG or farmer) that slipped under the radar due to incomplete sampling/bias towards certain countries?

Not too sure what you mean by a "follow-up". I'm right now spending hours daily only answering to emails, comments and such (not just here, mostly not here) so I have no time to write and work is piling up. I have at least three papers I'd like to write about soon[TM].

I think that the "teal" (Caucasus-like) component is a tell-tale of Indoeuropeans, at least in most cases (there may be a few Mediterranean exceptions though, in which it reflects some other kind of flow from Asia Minor maybe, Etruscan/Shekelesh-related?) It's a much more clear signature than the so-called ANE element, which does not overlap regularly with it and may have got other pre-IE or para-IE patterns of spread or even be some kind of ghostly signature that we would be better disregarding altogether maybe.

I do think that key evidence to address these problems will be found once Western Europe is properly sampled, particularly the Atlantic basin and particularly in the time-frame of Megalithism and Bell Beaker (Chalcolithic era). And by that I mean the Atlantic parts of the Iberian peninsula, France, Belgium and even maybe Germany (the Elbe is just a small region and can't be automatically extrapolated), as well as the Atlantic Islands. Scandinavia has also proven interesting (Gokhem particularly). I'd wish we have autosomal data for the Basque Country, Portugal, Brittany, Aquitaine, Britain and Ireland for the Chalcolithic particularly, the Low Countries, Saxony, Rhineland and Denmark too. So far we only have some suggestive mtDNA (mostly Basque, a few French and Portuguese) and, more punctually, some LTC data of great interest but limited scope. And the inlander Iberian samples that are interesting but not conclusive in any way (mostly unrelated to everybody else, looking like a cul-de-sac or extinct branch of the wider Early Farmers + HG admixture).

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